added distance command and filterseqs

[mothur.git] / ignoregaps.h

diff --git a/ignoregaps.h b/ignoregaps.h
index 8127b6205e42d18516561565e8a4eb29ccd56ab6..aa106c9b1bbc6bcc1cde4be9dd02fb5876b3ef85 100644 (file)
--- a/ignoregaps.h
+++ b/ignoregaps.h
@@ -27,7 +27,7 @@ public:
                int end = 0;
                
                for(int i=0;i<A.getLength();i++){
-                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
+                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
                        }
                        else{
                                start = i;
@@ -35,7 +35,7 @@ public:
                        }
                }
                for(int i=A.getLength()-1;i>=0;i--){
-                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.' || A.getAligned()[i] == '-' || B.getAligned()[i] == '-'){
+                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.' || A.getUnaligned()[i] == '-' || B.getUnaligned()[i] == '-'){
                        }
                        else{
                                end = i;
@@ -44,11 +44,11 @@ public:
                }
                
                for(int i=start; i<=end; i++){
-                       if(A.getAligned()[i] == '.' || B.getAligned()[i] == '.'){
+                       if(A.getUnaligned()[i] == '.' || B.getUnaligned()[i] == '.'){
                                break;
                        }
-                       else if((A.getAligned()[i] != '-' && B.getAligned()[i] != '-')){
-                               if(A.getAligned()[i] != B.getAligned()[i]){
+                       else if((A.getUnaligned()[i] != '-' && B.getUnaligned()[i] != '-')){
+                               if(A.getUnaligned()[i] != B.getUnaligned()[i]){
                                        diff++;
                                }
                                length++;